Referenced in

Retarded Animal Babies (2003)
(Video)
In RAB5 there is a fight scene where Hamster fights off dozens of rats and that fight resembles the same fight scene in the Matrix Reloaded where Neo fights all those Smith's

My Little Pony: Friendship Is Magic: A Canterlot Wedding - Part 2 (2012)
(TV Episode)
A musical cue from this film is heard when Twilight and her friends initially defeat the changelings en route to the Elements of Harmony. Additionally, the Changelings are defeated by the main characters bursting through a pile of them, sending then flying, much like how Neo escapes a mob of Smith clones.

Spoofs

Pootie Tang (2001)
The Burly Brawl scene in the Matrix Reloaded spoofs the scene where Pootie Tang battles all of his clones at the restaurant in the end. Most of the camera shots are very similar, and the way the clones attack both Pootie and Neo.